Deep sequencing of target linkage assay-identified regions in familial breast cancer: Methods, analysis pipeline and troubleshooting

Juan Manuel Rosa-Rosa, Francisco Javier Gracia-Aznárez, Emily Hodges, Guillermo Pita, Michelle Rooks, Zhenyu Xuan, Arindam Bhattacharjee, Leonardo Brizuela, José M. Silva, Gregory J. Hannon, Javier Benitez

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Background: The classical candidate-gene approach has failed to identify novel breast cancer susceptibility genes. Nowadays, massive parallel sequencing technology allows the development of studies unaffordable a few years ago. However, analysis protocols are not yet sufficiently developed to extract all information from the huge amount of data obtained. Methodology/Principal Findings: In this study, we performed high throughput sequencing in two regions located on chromosomes 3 and 6, recently identified by linkage studies by our group as candidate regions for harbouring breast cancer susceptibility genes. In order to enrich for the coding regions of all described genes located in both candidate regions, a hybrid-selection method on tiling microarrays was performed. Conclusions/Significance: We developed an analysis pipeline based on SOAP aligner to identify candidate variants with a high real positive confirmation rate (0.89), with which we identified eight variants considered candidates for functional studies. The results suggest that the present strategy might be a valid second step for identifying high penetrance genes

Original languageEnglish (US)
Article numbere9976
JournalPloS one
Volume5
Issue number4
DOIs
StatePublished - Sep 10 2010
Externally publishedYes

Fingerprint

High-Throughput Nucleotide Sequencing
breast neoplasms
linkage (genetics)
Assays
Pipelines
Genes
Neoplasm Genes
assays
Breast Neoplasms
Chromosomes, Human, Pair 6
Chromosomes, Human, Pair 3
genes
Penetrance
penetrance
methodology
Technology
Microarrays
selection methods
Chromosomes
Throughput

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Deep sequencing of target linkage assay-identified regions in familial breast cancer : Methods, analysis pipeline and troubleshooting. / Rosa-Rosa, Juan Manuel; Gracia-Aznárez, Francisco Javier; Hodges, Emily; Pita, Guillermo; Rooks, Michelle; Xuan, Zhenyu; Bhattacharjee, Arindam; Brizuela, Leonardo; Silva, José M.; Hannon, Gregory J.; Benitez, Javier.

In: PloS one, Vol. 5, No. 4, e9976, 10.09.2010.

Research output: Contribution to journalArticle

Rosa-Rosa, JM, Gracia-Aznárez, FJ, Hodges, E, Pita, G, Rooks, M, Xuan, Z, Bhattacharjee, A, Brizuela, L, Silva, JM, Hannon, GJ & Benitez, J 2010, 'Deep sequencing of target linkage assay-identified regions in familial breast cancer: Methods, analysis pipeline and troubleshooting', PloS one, vol. 5, no. 4, e9976. https://doi.org/10.1371/journal.pone.0009976
Rosa-Rosa, Juan Manuel ; Gracia-Aznárez, Francisco Javier ; Hodges, Emily ; Pita, Guillermo ; Rooks, Michelle ; Xuan, Zhenyu ; Bhattacharjee, Arindam ; Brizuela, Leonardo ; Silva, José M. ; Hannon, Gregory J. ; Benitez, Javier. / Deep sequencing of target linkage assay-identified regions in familial breast cancer : Methods, analysis pipeline and troubleshooting. In: PloS one. 2010 ; Vol. 5, No. 4.
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